Since thunderbolt basically is a PCI express cable, there's nothing to stop people from building external cases that can hold PCI express cards, like the Mac Pro can. Since thunderbolt is becoming prevalent across the line, I can't really see a need for the Mac Pro so much anymore.
True it is nice in some situations to put all your hard drives and all your PCI cards in one box, but at %2 of the total sales (by units) the big old tower is less relevant these days.
The other thing the Mac Pro had was the highest end of Intels CPUs. If the sales aren't making the engineering effort worth it, then the answer Apple's intending people to take may be a high end iMac.
I edit a lot of HD in Final Cut X on my 2 year old Macbook Pro, and background rendering seems to have no trouble keeping up. I've not really felt CPU constrained in awhile with HD.